Uncovering patterns of the evolution of genomic sequence entropy and complexity
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ORIGINAL ARTICLE
Uncovering patterns of the evolution of genomic sequence entropy and complexity Rafael Plana Simões1 · Ivan Rodrigo Wolf1 · Bruno Afonso Correa1 · Guilherme Targino Valente1,2 Received: 19 November 2019 / Accepted: 22 September 2020 © Springer-Verlag GmbH Germany, part of Springer Nature 2020
Abstract The lack of consensus concerning the biological meaning of entropy and complexity of genomes and the different ways to assess these data hamper conclusions concerning what are the causes of genomic entropy variation among species. This study aims to evaluate the entropy and complexity of genomic sequences of several species without using homologies to assess relationships among these variables and non-molecular data (e.g., the number of individuals) to seek a trigger of interspecific genomic entropy variation. The results indicate a relationship among genomic entropy, genome size, genomic complexity, and the number of individuals: species with a small number of individuals harbors large genome, and hence, low entropy but a higher complexity. We defined that the complexity of a genome relies on the entropy of each DNA segment within genome. Then, the entropy and complexity of a genome reflects its organization solely. Exons of vertebrates harbor smaller entropies than non-exon regions (likely by the repeats that accumulated from duplications), whereas other taxonomic groups do not present this pattern. Our findings suggest that small initial population might have defined current genomic entropy and complexity: actual genomes are less complex than ancestral ones. Besides, our data disagree with the relationship between phenotype and genomic entropies previously established. Finally, by establishing the relationship between genomic entropy/complexity with the number of individuals and genome size, under an evolutive perspective, ideas concerning the genomic variability may emerge. Keywords Shannon entropy of genomes · Comparative genomics · Genomic evolution · Genomic complexity · Biological complexity
Introduction Divergencies concerning the meaning of genomic entropy and complexity, and their evolutionary aspects, motivated the development of this study. First, we designed an approach to calculate the entropy of genomic sequences by adapting the Shannon entropy and skipping the homology Electronic supplementary material The online version of this article (https://doi.org/10.1007/s00438-020-01729-y) contains supplementary material, which is available to authorized users. * Guilherme Targino Valente [email protected] 1
Department of Bioprocess and Biotechnology, São Paulo State University (Unesp), Avenida Universitária, 3780, Botucatu, São Paulo 18610‑034, Brazil
Department of Developmental Genetics, Max-Planck-Institut für Herz- Und Lungenforschung, Ludwigstr., 43, 61231 Bad Nauheim, Hessen, Germany
2
searches. Afterward, we established correspondences between the entropies with non-molecular data of different species allowing new findings concerning the evolution of genomic entropy
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